Overload
by Lorr
Summary: Sheppard halted them at the foot of the stairs.  Elizabeth was between them, but he would only need to move his hand a couple of inches to aim the gun at either of the men.
1. Chapter 1

**Title:** Overload

**Author:** Lorr

**Genre/Rating:** Drama

**Characters:** Sheppard, Beckett, McKay, Weir, Ronon, Teyla, minor Lorne

**Disclaimer:** The Stargate universe and characters belong to a whole bunch of people that are not me. I'm here to play.

**Spoilers:** I don't think so.

**Note:** This takes place sometime during season 3 before Sunday. Reviews are always appreciated. Please be honest. Thank you for reading, and I hope you enjoy it.

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"Will he be ready?"

"I believe so."

"Believe so?"

The two men looked through a small window into a brightly lit room. One, of indeterminate age, was dressed in a very expensive dark suit. The other, an elderly man, wore a white lab coat. The room could easily be mistaken for the interrogation room in just about any police station in the country. It was small and furnished with a table and two chairs. It was also soundproofed.

Two men sat in the chairs, opposite each other. A middle-aged man dressed in a lab coat, sat with his hands folded on the table. He was calm, even emotionless. Facing him, a younger man slouched with his head bowed down. His eyes were almost closed, trying to avoid the light. He was listless. His hands and forearms rested flat on the table and he leaned on them for support.

"I told you, he's been very difficult. So much so, that I had to push the treatment well beyond safe levels."

"Safe? I take it you're joking."

"No, I'm not joking. I don't think he'd be much good to us if he were comatose or dead. We're taking a lot risks with him. I just can't absolutely guarantee that he'll do it. As I said, he's been the most challenging…" Lab coat paused. "Are you sure I can't have another day or two, just to be safe?"

"We gave you all the time we could arrange. That's why we sent the boy. He has the equipment and can make sure things go according to the plan."

"I'm sorry to lose him. He had a promising future."

"I know, but it was the only way."

"There was no trouble getting him in?"

"No. They have people transferring in and out on a regular basis now. We got him in on the last rotation. They needed a substitute. One of the techs assigned to go had an accident that will keep him out of action for a couple of months."

"Good. It's such a waste, though. I would have loved to have seen it."

"Me, too, but it can't be helped. The risks are just too great." The dark suit turned to leave. "You have 36 hours."

----------

Elizabeth was working late, as she often did. The Gate room and ops were quiet at this time of night, so she was able to get more done, significantly more. She didn't even notice the Marines leaving the floor below. To be honest, she rarely noticed their presence any more unless they were needed. The quiet patrols weaving through the area were now part of the wallpaper.

The lights going down indicated anything was amiss. The emergency lighting came up. She hurried out of her office to find the two on-duty technicians standing at the railing, looking down. The entire Gate room was in shadow. It was also the middle of the night, so almost no light penetrating the windows. She glanced out and saw the entire city was darkened then looked back down to see a figure standing near the Gate.

"What's going on?" Elizabeth asked to two technicians. They had returned to their stations and were frantically typing on laptops.

"Don't know, Ma'am." One responded. "We're locked out. Nothing's working."

She blinked as her eyes became used to the gloom then started down the stairs. The figure was suddenly familiar. "John? What are you doing?"

He shook his head and mumbled something she couldn't catch. It was only when she got to the bottom of the stairs that Elizabeth could see his left hand was on the small console first raised by Helia on her arrival in Atlantis such a short time ago. She jumped when the emergency alarm started to blare loudly.

"What are you doing?" She raised her voice in an effort to keep a growing fear out of it.

He was watching her even though he did not take his hand from the ATA pad on the console.

"I have to." He was barely audible over the alarm.

"John, what's going on?" She hurried to where he stood.

"Stop," Sheppard said as his right arm jerked up. It held his pistol and the weapon was pointed at her. His voice was almost unrecognizable. It was distant and strained. "I have orders. Turn around and take one step backwards to me. Slowly."

Elizabeth did as he instructed. He held the pistol to her back and she felt the muzzle touch her shoulder.

"John, what are you doing?" She tried to look over her shoulder.

"Don't move." The gun pushed gently against her. His eyes flicked up to the technicians. "Turn off the alarm and come downstairs. Make it fast."

The silence was almost like a blow to the body. Moments later, the young men descended.

"Stop." Sheppard halted them at the foot of the stairs. Elizabeth was between them, but he would only need to move his hand a couple of inches to aim the gun at either of the men. "Stay there and don't move."

"John. Listen to me."

"Tell them to stay there." There was something chilling in his tone that left her with no doubt that he would shoot.

"Do as he says." She told them. "What orders, John?"

"Dr. Weir, Col. Sheppard, this is McKay. We've lost power to all systems in the city." McKay's voice on their ear transceivers sounded frantic. "What is your status?"

"John?" She was only marginally relieved that McKay had contacted them.

"Answer him."

Elizabeth tapped her transceiver. "Rodney?"

"Elizabeth? What the hell is going on?"

She licked dry lips and tried to stay calm. "Col. Sheppard has taken control of the city."

"What? How?"

"He's raised the console Helia used, Rodney."

"Why?'

"I don't know."

"What is he doing? Where are the Marines?"

"I don't know, Rodney. He won't tell me anything." She thought she heard pounding and searched the shadows as much as she could without moving. Every door was closed. "I think the Marines are locked out."

"Tell them to stop." Sheppard said quietly.

"I'm sorry?"

"Tell whoever it is trying to break in to stop."

Elizabeth thought as fast as she could. Hoping she could change Sheppard's mind and have him reverse what he had done, she nodded. "This is Weir. Whoever is trying to break into the Gate room, stop immediately."

The faint sound of pounding outside halted.

McKay demanded, "Sheppard? What are you doing?"

"John, please stop."

It was several seconds before he spoke. The edge of strain was more pronounced and he was breathing heavily. "I have to do this. Orders."

"What do you mean?"

This time, he didn't answer.

"Sheppard, what the hell are you doing?"

"Shut up, Rodney," was the Colonel's only response.

"What are you…?"

"Rodney, please!" Elizabeth almost shouted. Something in her voice silenced the astrophysicist.

She knew it was only a few minutes, but it seemed like an eternity before the pressure of the muzzle against her back disappeared.

"John?"

"I'm sorry. I had to."

She slowly backed away as she turned. Sheppard was staring at her, his weapon hanging limply at his side. "What have you done?"

"I had to...Orders." He pulled the transceiver from his ear.

Elizabeth heard a click. The gunshot that followed was almost deafening, but it was the sound she heard less than an instant later that made her sick. She shouldn't have been able to distinguish the sounds, but was certain she did. It was the wet thwack of the bullet hitting flesh. It wasn't until Sheppard staggered that she realized he was wounded. His gun clattered to the floor then his knees buckled beneath him.

"No!" She spun around to look back at the technicians. "Ken, put the gun down and come help me. Jeffrey, get the first aid kit."

One of the techs nodded and ran back up the stairs. The other, the one that had fired the gun, was frozen to the spot. He seemed to be unable to move. He stared at the pistol cradled in both hands.

"Ken. Put it down!" Elizabeth shouted as she dropped to her knees next to Sheppard.

The young man shook his head once and quickly brought it up to his temple. Before she could move, the he pulled the trigger.

"No!" Elizabeth said it quietly, knowing it was too late.

Jeffrey stopped at the top of the stairs and stared down.

"The first aid kit!" She yelled at him. He disappeared through the consoles on the ops floor.

"Oh, God." Sheppard grabbed her arm as he fought for breath. "Help me…help me up."

"No. Don't try to move." Elizabeth held him down. He'd slid down to the floor, supported by the console. Leaning on his left hand with the arm locked straight, his right hand clutched a wound low on that side of his chest. Blood oozed between his fingers.

"What was that? What's happening?" McKay's voice was frantic.

"Rodney!" Elizabeth interrupted him. "You have to get the doors open. John's been shot. Ken Richardson shot him then killed himself. We need a medical team in here fast."

"Dammit. I can't. Nothing's responding. He's locked us out of everything. Hold on."

Jeffrey ran down the stairs with a bright orange canvas bag, slowing as he passed the body of his colleague. The pounding on the doors started again, causing the young man to glance over his shoulder. He ran to Elizabeth and Sheppard and dropped to one knee then began to dig through the kit.

"Oh my God, here we go again. "McKay's voice made her jump. "Elizabeth, he's set the ZPM to overload."

"What? How long?" Elizabeth was having trouble understanding the events of the last five minutes. She shook her head and unwrapped a pressure bandage.

"Damn it! Nine minutes, twelve seconds."

"Can you do something?"

"I don't know. Like I said, Sheppard's locked us out. He crashed almost all systems and scrambled the access codes. How the hell…"

"Does it matter?" Zelenka's voice asked.

"Yes! No. Wait. No, no, try that." She heard McKay yell at someone else. He paused again. She could hear frantic typing on keyboards. Finally, he spoke to her again. "Elizabeth, we don't have enough time. I don't think an entire day would be enough to unscramble this mess."

Sheppard made an effort to straighten and pushed his transceiver into Elizabeth's hand.

"The orders. They…said…Wraith coming. Listen"

"Rodney, can you remove the ZPM?" She was desperately trying to think.

"No, we can't even get to it. He's sealed the doors leading to every strategic area in the city. Damn! I don't believe it."

"Keep trying." She shook her head as she took the transceiver. "John, what orders? There were no orders."

"Listen." His voice cracked.

Elizabeth held the transceiver to her ear and listened. She stared at him in confusion. "John, it's just static!"

"No, isn't. Help me." Sheppard swallowed hard. He tried to move on his own when she hesitated. "I…can stop it!"

His thin black T-shirt and lightweight trousers soaked up relatively little of the blood seeping through his fingers. He was already sitting in an expanding pool that appeared black in the dim light.

Elizabeth quickly unrolled the bandage. "You're going to bleed to death. Let us get this on you first."

"Hurry." He ground out between clenched teeth then groaned as Jeffrey leaned him forward. Elizabeth quickly wrapped the bandage around him and tied it off.

"We need to get him up."

"Yes, Ma'am."

She took one arm and nodded at him. Jeffrey grabbed his other arm and they lifted him, both certain he would pass out before they could turn him to face the console. He groaned loudly as they moved.

Sheppard clung to the console, the blood he stood in making the floor slippery. A cold sweat formed over his entire body and the room started to spin lopsidedly. His blood smeared the surface of the console as he moved his hand to the ATA sensor. He leaned on it and closed his eyes while he tried to catch his breath.

"Hold him!" She adjusted her grip as Jeffrey took more of his weight.

"John?" Elizabeth feared it was too late. He shook his head a fraction.

"What's going on?" McKay's voice startled her.

"John's trying to stop…"

"Are you serious? He's the one who…"

"Shut up, Rodney!" She cut him off.

They waited long seconds that turned into a minute then two. Sheppard was gasping for breath, and it frightened her. She glanced up at the technician. Jeffrey was pale and kept looking back at the body at the foot of the stairs, but he held the colonel securely.

"John?" Elizabeth asked quietly.

He clung tightly to the console.

"What is he doing?" Even though he whispered, McKay's urgent tone startled her. He was not accustomed to waiting for others to do what he considered his job. He was also fearful of what was about to happen.

"Rodney." Elizabeth whispered back. "Wait."

"I can...minute…need minute." Sheppard coughed and fought to stay conscious.

"He needs just a minute." She repeated.

"That's just it. We only have four minutes and twenty seconds."

Each second seemed to take minutes and flew by at the same time. One minute passed, then two. Sheppard suddenly slumped over, no longer able to support any of his own weight. Elizabeth and Jeffrey struggled to hold his dead weight and carefully laid him on the floor. He was barely conscious.

"Má bůh! He's done it!" Zelenka shouted. "Rodney, Col. Sheppard's done it!"

"Yes, yes. I can see that." McKay yelled at Zelenka then lowered his voice to speak to Elizabeth. "Sheppard stopped the overload and released control of the systems."

"Why aren't the doors opening?" She looked from one closed door to the next then around the Gate room. "The lights haven't come on, either."

"He only stopped the explosion. We have to reinitialize everything else."

"Rodney! Open the doors!" Elizabeth shouted at him. She pressed her hand against the bandage in an effort to staunch the bleeding. "John, stay with me. Open your eyes."

Sheppard tried to keep his eyes open, but they knew he was losing the battle.

The astrophysicist was immediately contrite. "Oh, God, yes. I'm sorry. Uh. Done."

Every door on the level opened at once. Two dozen Marines rushed in from different directions. Beckett and his medical team entered with the two gurneys stored near the Gate room for emergencies. The doctor pointed to the body at the foot of the stairs as he hurried past. Two medics stopped there along with three of the Marines. Beckett continued with the rest of his team to where Sheppard lay. Elizabeth and the technician moved back to allow them in.

"Quickly." Beckett didn't need more than a glance at the colonel and the floor around him to know there was little time. It took just a few seconds for the team to check for an exit wound, slip an oxygen mask on Sheppard and get him onto the gurney. They were soon racing to the corridor leading to the infirmary.

Beckett paused in front of Elizabeth momentarily. "Elizabeth, I want you and Jeff to come with me, too."

"Carson…"

"I don't have time to argue. There are plenty of people here to look after things. Now!" With that, he ran after the gurney.

"Go ahead, Dr. Weir. We have things under control." Maj. Lorne stopped next to her.

Elizabeth looked at her hands. Blood dripped from them. Her mind did not want to process the last ten minutes, she wanted to do something, but she nodded and followed the doctor with the young technician.

----------

Beckett caught up with the gurney within seconds. Dr. Keller was running alongside of it, holding a thick pad of gauze against Sheppard's wound. Blood already stained her gloved hand. They turned into the infirmary and began to work on the wounded man.

"There's a single gunshot wound to the upper right quadrant of the abdomen. No exit wound is visible." Beckett said as they halted the gurney. "He's already lost close to three units of blood, and probably more internally. Hang two units and make sure we have another eight typed and matched."

The radio conversation from the Gate room gave the infirmary time to prepare for Sheppard's arrival. Beckett's staff knew their business and needed little instruction. In seconds, the colonel's clothing was cut away and discarded. A nurse started the blood transfusion while another applied the pads for the heart monitor and an automatic sphygmomanometer, activating both.

She read the screens as the vitals became available. "Heart rate is 118 and BP is 83 over 56."

"Colonel? John? Can you hear me?" Beckett leaned close to Sheppard's face. His eyes rolled open for only a moment.

Beckett turned to the wound and cut away the blood-soaked dressing. Someone held a thick pad of gauze ready. The old dressing was carefully removed, revealing a medium sized hole that immediately oozed an alarming amount of blood. The doctor swore under his breath.

"Doctor, his BP is dropping fast, 76 over 51."

"He's bleeding out. We need to get him into surgery."


	2. Chapter 2

"What the hell was he doing?" McKay demanded as soon as he entered the infirmary. His voice was angry, but his face told a different story. He was worried, and scared. One of the very few certainties in his life was shattered. He relied on Sheppard's calm steadfastness from that first day in Antarctica. The anchor was gone, and McKay was having trouble grasping that knowledge. He stopped and looked from Teyla to Elizabeth. Now his voice was quiet. "How is he?"

Elizabeth shook her head. "Still in surgery."

"Have you been able to repair the damage, Rodney?" Teyla asked quietly.

McKay looked at the datapad he carried and shook his head. "Not yet. Unless Sheppard can tell us exactly what he did, it's going to take us a day or two. We have to run diagnostics on everything we reinitialize."

"Why?"

"Sheppard crashed every major and most secondary systems in the city, probably to prevent me from interfering with what he was doing." McKay dropped his data pad onto a table and began to pace back and forth. "When he reinitialized the power controls he didn't do it in sequence or use the correct procedures. He hammered the proverbial square peg into a round hole to over-ride what he did to the ZPM. I'm amazed that he was able to stop the overload and keep the ZPM from exploding much less get anything else back online. Until we…"

"Thank you, Rodney, we understand." Elizabeth held up a hand to stop him. Her head hurt and she was tired. "What we need to do now is find out why John tried to destroy the city."

"And probably about three quarters of this solar system along with it."

Teyla added, "We also need to determine why the technician shot John and killed himself."

Elizabeth nodded somberly and held a small container out to McKay.

"What's that?" He asked as he opened it and saw the transceiver. It was still stained with blood. He frowned at it then her.

"John gave it to me just before Richardson shot him. He wanted me to listen, but it sounded like it was just static."

McKay closely examined the transceiver. His brow furrowed deeply as he squinted at the ear loop. "What the hell?"

"What is it, Rodney?" Teyla asked.

"I don't know. I'll check it out." He picked up the data pad and hurried out.

The two women waited in silence. They were too confused and worried to talk, but the wait wasn't long. Within minutes, Beckett came through the door. They stood up and he raised a hand to wave them back to their seats.

"Sit down, sit down."

"How is he, Carson?" Elizabeth asked.

"Alive. He's in critical, but stable, condition." Beckett ran a hand through his hair and exhaled heavily. "We performed a laparotomy. The bullet transected a small branch of the portal vein in his liver, which caused the hemorrhaging. We barely caught it in time."

"He'll be alright?"

"Barring complications, I believe so. Like I said, he's stable, and we're still transfusing him. There was a bit of damage, but the liver is the one organ in the human body that can regenerate." Beckett paused. "I had to put in a drain and pack the wound in the liver, so I'll need to go back in…"

"Excuse me?" Elizabeth was dumbfounded.

The doctor raised his hands to stop her. "Listen. It's okay. The liver is full of blood vessels, so some bleeding is possible, and there could be bile seepage. I'll go in and close it up properly once I'm sure there is no seepage and the bleeding has completely stopped."

"When?" Teyla asked.

"Two or three days." He gave them an encouraging smile. "Please don't worry. It isn't unusual with this type of wound."

The two women looked at each other, uncertain about the explanation. Nothing seemed to be making sense today.

Beckett had a question he didn't want to ask, but asked it anyway. "Elizabeth, what happened?"

She shook her head slowly. "I don't know, Carson. I haven't seen much of John since he came back from Earth. I know he looked exhausted, but he just said they put in long days."

"He did appear to be quite weary, even a little unwell. He has been…distant since his return." Teyla said thoughtfully. "I had the impression something happened that John was unwilling, or unable, to talk about."

"Dr. Beckett?" A young woman hurried over to Beckett with a data pad. She offered it to him. "I think you should see this."

He took the pad and read the screen. "Are you sure?"

"Yes, Sir."

"Okay, see if you can find out exactly what it is. Quickly." He gave the pad back to her.

"Yes, Doctor. We're already working on it." She nodded and left.

"What is it?" Elizabeth stood up again.

"It's preliminary, but it looks like John has at least one unknown drug in his system, possibly more."

"Drugs? What for?" Elizabeth's hopes that the nightmare would not get any worse disappeared.

"I don't know." He paused and exhaled loudly. "Elizabeth, what did he go back to Earth for?"

"Some of the military brass wanted to talk to him. There was something about a couple of the missions John was on with the SGC, and they wanted to discuss weapons and tactics." She shook her head. "They didn't give me very much detail. You know how the military can be."

"Aye. I do. Well, it could be that someone wanted him there for something more than just a debriefing." He said with a grim set to his face. "We need to find whatever it is he was taking."

Elizabeth turned to her young friend. "Teyla, will you and Ronon search his quarters, please?"

Teyla hesitated then bowed her head a fraction. "Yes, of course."

"Thank you." Elizabeth turned back to Beckett. "Can we see him?"

Beckett shook his head. "He'll be in recovery for a while. I'll let you know when he's awake."

Elizabeth and Teyla started for the door, but Elizabeth turned back to him. "Carson, I'm going to order around the clock guards on John. I don't want him leaving the infirmary alone."

He was taken aback. "Do you really think that's necessary? I can have someone with him at all times."

"Yes, I do. John tried to destroy the city. He may be under the influence of some unknown drugs. Carson, until we know what's going on, I can't take any chances."

Beckett nodded. "Very well. Tell them to come see me first."

----------

Elizabeth walked out of her office to Gate ops. She glanced toward the window. It was full daylight outside, late afternoon to be precise. MacKay was working on one of the Ancient consoles and a laptop at the same time. Zelenka was at another console. Three technicians manned other positions nearby. Each was engrossed in their work.

"Rodney?"

He turned and blinked wearily at her. "Yeah?"

"How's it going?"

He looked around. "We're getting there. So far, it's just been a matter of running diagnostics and reinitializing systems. We've gone through the major systems. The shield, cloak and weapons chair are working. Water and the transporters will be back in an hour or two."

"Power to some areas is still offline or intermittent, but we should have everything sorted out in twelve to fifteen hours." Zelenka added.

"That's good." She was relieved at the news. It was better than she had hoped for. "Were you able to find anything on John's transceiver?"

McKay looked lost for a moment, the sleepless night and anxiety were catching up to him. He turned to another computer and quickly entered something Elizabeth didn't catch. "Oh, yes. There's a second receiver on it. I took a chance and examined Richardson's transceiver as well. They both were, and still are, receiving a transmission being broadcast on an unused frequency."

"Who was transmitting it, and where from?"

"We don't know who. Maj. Lorne's looking for the transmitter now."

"What was it saying?"

"Ah, I'm still working on that. I don't think it's just static. McKay tapped a key on the laptop. He paused then quickly typed several more. "Hmm. That's odd."

"What?" Elizabeth tried to read the screen over his shoulder.

"It looks like the transmission is layered." He frowned at the screen for several seconds. "Huh! It may be a subliminal message."

"Can you tell what the message is?"

"Not yet, but I will."

"Elizabeth?"

She turned to see Teyla and Ronon climbing the stairs. Their expressions were clouded and the Athosian carried a small cloth bag.

"Come into my office."

Once inside, Elizabeth turned to them. "You found something?"

Teyla opened the bag, pulled out a standard pharmacy bottle and handed it to her. She opened it and looked inside. It was half full of small, white tablets. Elizabeth closed the bottle and gave it back to Teyla.

"Thank you. Would you take it to Carson, please?" She started to walk around her desk to sit but turned back. "Wait. Search Ken Richardson's quarters as well."

"You think he's involved?" Ronon asked.

"Yes, his transceiver was the same as John's. He's also a civilian and has been here for only a couple of weeks. He shouldn't have had a gun, and why did he kill himself?"

"We will take these to the infirmary and search Richardson's quarters immediately."

----------

"He's just coming around." Beckett pulled her aside. "Elizabeth?"

"What is it?" His expression worried her even more.

"I'm a little concerned. John almost destroyed the city and he's been on some unknown drugs. On top if that, he's been severely wounded. This is a lot to deal with. Don't be surprised if he's extremely disoriented."

She bit her lip and nodded. "Of course."

He led her through the infirmary to Sheppard's room. Two armed Marines stood outside the single entry. Elizabeth knew too well what the equipment was and understood their functions. The heart monitor and pulse oximeter were quietly performing their roles. An oxygen cannula looped over his face.

She hesitated momentarily at the door as a nurse pulled a blanket up over a very large surgical dressing covering much of the right side of his abdomen and lower chest. A tube emerged from the edge of the dressing and disappeared off the edge of the other side of the bed.

The nurse picked up a data pad and walked over to Beckett. "His vitals are holding, Doctor. He opened his eyes a moment ago, but didn't say anything."

"Thank you, Susan." Beckett took the pad and quickly scanned it as she left.

Sheppard's eyes were closed but his right hand moved slightly. An IV of clear fluid was attached to the back of the hand. A half-empty unit of blood was still transfusing into his left arm. The heart monitor beeped softly, but steadily. They heard a slight increase in the beeping as they approached the bed.

"John?" Beckett reached out and touched his shoulder.

"Hmm." Sheppard opened his eyes then closed them tightly. He turned his head away. He trembled as he tried to breathe through the pain and dizziness.

Beckett reached up and turned the off the light over the bed. "Don't move, son."

He quickly glanced at the doctor. "Wha' happen'd?"

"You don't remember?" Elizabeth asked.

His right hand moved to the source of the pain as he blinked at them. The monitor beeped even faster. "Shot? Who…?"

They could see he was trying to get his mind to work, to remember. Beckett tried to divert him. "John, you just rest. We can talk later."

He struggled to get up, pushing the blanket down as he turned to one side and tried to pull off the oxygen cannula. His voice was slurred. "No! Gotta stop..."

"John! It's okay. You already did. The city is safe." Elizabeth grabbed his hand to get his attention while Beckett held him down. "You stopped it. The ZPM is not going to explode."

Sheppard moaned softly as slumped back with his eyes closed and brought a shaky hand to his face. A cold sweat appeared on his skin and he began to shiver. Beckett pulled the blanket up.

"Susan!" The doctor called to the nurse. She appeared instantly. "Bring another blanket, love. Quickly."

"Carson?" Elizabeth tried to hide her alarm.

"This is what I meant."

"How?" He squinted and tried to shield his eyes against the remaining light.

"John, listen to me. Everything is alright." She smiled warmly when he focused on her. "We're still here, aren't we?"

He turned to Beckett as the doctor pulled the second blanket over him. They could see him trying to understand what was going on. "Yeah. Here."

"John, we think you were drugged."

"Drugged? Hunh?" The effort had drained all of Sheppard's energy. The fog in his brain made it so difficult to follow what they were saying.

"We think something happened to you back on Earth." Beckett added.

"Earth?" Muffled flashes of memories crowded in. The lingering effects of the unknown drug in his system, as well as an oppressive headache and the pain in his abdomen made it impossible to string them together in any coherent way. His mind refused to cooperate. All he could do was repeat, "Earth?"

Beckett could see that he was drifting away. "It's okay, son. We'll talk about this later."

Sheppard's eyes closed and the shivering began to subside. He was asleep again.

Beckett lifted the blanket to examine the dressing. Satisfied that no damage was done, he spoke quietly to Susan before he and Elizabeth left the room. The nurse remained as they walked out, busily checking vitals and the IVs again.

Elizabeth glanced over her shoulder as they entered his office. This frightened her. "He's going to be alright, isn't he, Carson?"

Carson thought for a long moment before answering her. "I hope so. Teyla and Ronon brought me the tablets from John's quarters. They found what appear to be the same tablets in Richardson's quarters. The lab is testing them right now. They look like generic antibiotics, but who knows?"

"Did John have an infection?"

"Not that can I tell, but it would be a good excuse to have him take something over a specific period of time. Anyone seeing them wouldn't think twice about it."

"So he would have been under the influence of whatever it is for this entire time." She rubbed the tension in the back of her neck. "How long before you know what these things really are and what they did to him, them?"

Beckett compressed his lips and shook his head slowly. "It's hard to say. It is similar to some of the psychotropic drugs. Apart from that, I have no idea what it is. I've never seen this one, and, as far as I know, no-one else has either."

"What? Where is it from?"

"It hasn't been approved by the FDA or any other agency, and it isn't one of the military's secrets. That I know of, anyway." He shrugged. "I don't see how it could be from any other source."

"Dr. Weir, this is McKay." The astrophysicist's voice came over her transceiver. She tapped it.

"This is Weir."

"Can you come to my lab? I think you should see this."

"I'll be right there." She squeezed Beckett's arm. "Thank you, Carson. Please let me know when he wakes up again."

"Aye, love."

----------

McKay looked up as Elizabeth walked into his lab. He held up something. "Take a look at this."

"What is it?" It was difficult to see that it was a transceiver until she was closer. What she could easily see, though, was that McKay was subdued, thoughtful, definitely not his normal self. "Is that John's radio?"

"Yes. Look closer." He pulled over a magnifier lamp and switched it on. She was grateful to see the blood was gone. He pointed to the loop that fits over the back of the ear. "See that? It's a second receiver. Richardson's is the same."

She took it from him and turned it over and over under the glass, frowning at it. "Where was the signal coming from?"

"This." McKay pulled over a personal digital music player. A thin cable led to a pair of speakers.

"What is it?"

"Just what it looks like, actually. It has some modifications, though." He picked it up and pressed a tiny button on the side.

"What is it?" Elizabeth raised an eyebrow at him. "Was that what John was listening to in the Gate Room?"

"Yes again. The casual listener would hear only the white noise. Apart from it being annoying, they wouldn't give it a second thought. But what's underneath?"

He turned off the noise and flipped a switch on a nearby recorder. The noise abruptly stopped and was replaced by tapping. McKay watched her as she tried to place the sound. It took only a couple of seconds before she turned to stare at him.

"Is that Morse Code?"

"Yep. Well, sort of. It's a code of some kind."

"Do you know what it says?" She asked hopefully.

"Not quite." He turned off the recorder and glanced at a large box of the personal effects found in the dead man's room. "Lorne and Ronon brought a whole box of stuff from Richardson's room."

"Will it take long to go through it?"

"Don't know," he said then glanced at her, "shouldn't."

"How are the repairs going?"

"All essential stuff is done. We're down to minor systems and equipment. Stuff in the labs, that kind of thing. Radek's working on it and I'll get back to it when I've finished here. We should be finished in a few hours." He looked as if he wanted to say more, but couldn't get it out.

"What is it, Rodney?" Elizabeth asked, even though she had a good idea what he was thinking.

McKay unplugged the MP3 player and moved the speakers. He was trying to get his head around the fact that it wasn't Sheppard standing there talking to him. It was always Sheppard. But, now, it was his friend that nearly killed them all, his friend was the enemy. He swallowed. "How is he?"

Elizabeth understood how he felt. "Carson said he came through the surgery pretty well. He woke up, but only for a minute."

"What's the prognosis?"

"I don't know." She paused. "John was on Earth for eight days. Carson thinks he's been drugged with some kind of mind altering concoction."

He was hesitant.

"Rodney, we don't know what happened to him while he was gone. You know he would never do this of his own volition. We have to find out what they did to him. Okay?"

McKay was silent for a long time. She knew he was trying to come to a decision. He did, and suddenly, he seemed to find energy again. "Yes, yes, of course you're right. Unless you need something else, I'll get back to it."


	3. Chapter 3

"I know a little more about the drugs John was on, well at least one of them." Beckett said as he folded his arms over his chest. He had the complete attention of his small audience of Elizabeth, Teyla and Ronon. "I'm now certain it's a very potent psychotropic drug."

Teyla frowned. "What does that mean?"

"Psychotropic drugs act on the mind. They're normally used to treat depression, anxiety, psychoses and any number of mental illnesses."

The young Athosian was appalled. "There is nothing wrong with John, is there? Why would he need such a drug?"

"No, of course there wasn't any reason for him to be taking it."

"Then, why would he take it?" Ronon asked.

"I'd be surprised if John even knew what it was."

"You said drugs. What else?" Elizabeth folded her arms in an effort to keep herself from shaking with anger.

"We're still working on those. It looks like he hadn't been given any of those for two or three days, so they are already breaking down in his system."

Elizabeth asked the next question on their minds. "Will there be long term affects?"

"I don't know."

"How is John doing?"

"Still critical, but his vitals are stable. He is improving."

"Okay. Thank you, Carson." Elizabeth started for the door. "You'll keep me informed?"

"Of course." Beckett smiled tiredly at her as she left then looked at Teyla and Ronon. "I take you two want to see him?"

"Yes, please, if it is alright." Teyla smiled tentatively.

"I don't know when he'll wake up again, or what his state of mind will like be when he does."

"What do you mean?" Ronon frowned.

"He's been disoriented, confused. I believe it is being caused by the drugs as well as the trauma of the gunshot wound." Beckett thought for a moment. "It might do him good to have some familiar faces around."

----------

Sheppard woke with a start, struggling to sit up. Pain and instant dizziness forced him back before anyone could reach out to stop him. He tried to keep his eyes open, but that just made the room spin faster and at wildly impossible angles. He closed them again and clutched the edges of the mattress, knocking the pulse oximeter from his finger. Voices drifted haphazardly through the waterfall that seemed to be cascading in his head.

"John? Can you hear me?" Beckett felt for the pulse in the colonel's left wrist. It was fast, but strong. He watched as Sheppard fought for control. After a moment, he gently closed his hand over the entire wrist. "John?"

"Yeah," Sheppard choked out. "ZPM?"

"Everything is fine."

"Safe?"

"Yes, it's safe. The city is safe."

The drunken room was beginning to regain its equilibrium. Sheppard released his grip on the mattress. He swallowed and carefully opened his eyes, grateful that only a single, dim light was on. He saw Beckett at his bedside, concern in his eyes. Something else was there for an unguarded moment. Was it fear?

Teyla and Ronon stood further away. Each of them wore carefully placed masks, expressions that could not be read.

Beckett reattached the oximeter and quietly asked, "How are you feeling?"

Sheppard blinked at him. He could not shake the memory that crowded out almost everything else in his head. His entire being protested the idea that he'd come within two minutes of obliterating everything he cared about. For a moment, he'd hoped that it was all just the shattered remnants of a nightmare, pieces of shadows lurking on the edge of his mind. But it wasn't. These shadows were never going to fade

"John?"

"M'okay." He finally responded as he looked away. He vaguely remembered the man who shot him. What was his name? Sheppard just remembered the man's eyes as he pulled the trigger. They were the eyes of a man who knew he was dying.

"How is the pain? If you need…"

"No drugs." He said as his fingers gingerly touched the bandage covering the wound. "Who shot me?"

"You were shot by one of the Gate technicians. There was a bit of damage to your liver, but you should recover completely." Beckett realized his patient wasn't listening to him. Instead, Sheppard was staring at the wall.

Beckett glanced at Teyla and Ronon. The concern for their friend was now clear in their eyes.

"I think you should go now. You can visit later."

They quietly turned to leave.

"Guard." Sheppard's voice was rough. "Post a guard."

Teyla turned back. "Elizabeth already did so, John."

"Good." He said as his eyes closed.

----------

Elizabeth looked at the people around the conference room table. She felt they needed a more secure space than her office to discuss the situation. McKay and Zelenka were scanning the room for listening devices as she, Teyla, Beckett, Ronon and Lorne watched. Kate Heightmeyer quickly entered and sat down. The doors immediately closed with a soft thud.

Beckett fidgeted with the data pad in front of him. He was visibly uncomfortable. His brogue accentuated by the anxiety. "This is so cloak and dagger. Am I the only one that feels paranoid?"

"We're clean." McKay glared at the doctor as he and Zelenka sat down.

"It is quite disturbing, Carson." Teyla supported him.

"Thank you." Elizabeth looked around the table. The room was tense, everyone feeling like they were holding their breath. They were all tired. No-one had slept since the alarm sounded at 0127 hours that morning and it was now night again. She looked at Beckett. "What is John's condition?"

"Well, I've been able to upgrade him from critical to serious. His vitals have remained stable and his blood volume is nearly back to normal." The doctor paused, glancing around the table. "However, he is experiencing withdrawal."

"Withdrawal?" McKay grimaced. The memory of withdrawing from the Wraith enzyme was never very far away.

"Is it serious?"

"Yes. It is serious, but there is someone with him at all times."

"Wouldn't it be better to slowly reduce the dosage?" Elizabeth asked. "Wouldn't want John and Richardson had be enough?"

Beckett shook his head, mouth compressed grimly. "Maybe, but I don't think it would be advisable. If this John was taking these long term and I knew exactly what they were, I'd be more likely to try it. These drugs were used to reinforce a suicide mission. He needs to be clear of them as soon as possible."

"Do you know any more about the drugs, Carson?"

"No, but I do know that, used in conjunction with other drugs and intensive…um…therapy, they would influence even the strongest mind."

"John was gone only eight days. Is that enough time?"

"I believe it would be, Dr. Weir." Kate responded first. "We would need to know more about the drug's effects and whatever Col. Sheppard was subjected to when he was on Earth to know for sure."

"We spoke with John a little while ago. He's having difficulties remembering where he is when he wakes up. His memories of what happened while he was on Earth are almost nonexistent. He remembers talking with Gen. Landry. After that, nothing."

"What was he there for?" McKay interrupted.

Elizabeth compressed her lips and shook her head. "I don't really know. Landry said that there were some people from the Air Force and the IOA that wanted to talk to him about a couple of the missions from when he was on Earth. They also wanted to go over our tactics, weapons and the Wraith ships. They weren't too specific. Does he remember anything else?"

Kate checked her notes. "He barely remembers arriving. He was probably given the first dose of this drug before he boarded the plane at the SGC."

Beckett took up the story. "When I asked him about the pills, he said that he came down with a throat infection. A doctor prescribed them."

"He didn't have an infection, did he?" Ronon asked, even though they all knew the answer.

"I seriously doubt it. That was probably just a story to get him to take the stuff."

Do you think John will be able to remember what happened?" Elizabeth looked from Beckett to Kate.

The psychologist answered her. "Perhaps. I wouldn't count on it, though. He was most likely heavily drugged for much of the time. It would leave him open to manipulation."

"Brainwashing." McKay finally said what they were thinking.

Ronon frowned at him. "Brainwashing?"

"As it appears to be in this case, it is forcing someone to do what they would not normally do by using propaganda, drugs and other means." Kate explained simply.

"Appears?" McKay was indignant for his friend. His eyes narrowed. "Sheppard would no more…"

"Yes, Rodney, we know John would never willingly try to destroy Atlantis or hurt anyone here." Elizabeth stopped him.

"I'm sorry, Dr. McKay, I didn't mean that Col. Sheppard was…"

"It's alright, Kate. We understand." Elizabeth looked at McKay. "Rodney, what have you found out?"

McKay pushed forward a small black box the size of a cell phone on the table. "We found this attached to the back of Sheppard's CD player in his quarters. It must have been put there in case he had the transceiver off when it was time to…do it."

"Have you been able to figure out what it's saying?" Ronon asked as he frowned at the device.

"No, just that it's some kind of repeating code." McKay hated having to admit that he hadn't figured it out yet. "I'm still working on it."

"Richardson was listening to the same thing?"

"Yeah."

"He had the same drug in his system." Beckett added. "I asked Dr. Biro to check for it when she performed the autopsy."

"What else do we know about him?"

"Nothing." Lorne spoke for the first time. "He's been here only a couple of weeks, and kept to himself. The people I talked to said he just seemed to be shy. His record doesn't indicate anything out of the ordinary. No-one would give him a second glance."

"Perfect cover." Ronon observed. "But, why did he shoot himself?"

"Question is, why did he shoot Sheppard?" McKay threw in. He looked at Becket and Kate.

Beckett nodded at the psychologist so she answered both questions. "We believe he shot Col. Sheppard to prevent him from reversing the overload of the ZPM. He probably meant to kill the colonel outright. He was also probably instructed to kill himself immediately, even though the city was supposed to explode."

"Well, by shooting Col. Sheppard, Richardson probably saved us all. The shock of being wounded is what most likely broke the hold of the programming."

"Oh, my God." McKay suddenly sat straighter and snapped his fingers. "They turned him into a za'tarc!"

"A what?" Ronon asked.

"Well, like a za'tarc." McKay qualified his diagnosis. He looked around the table. "The Goa'uld had the technology to program humans to do precisely the kind of thing that Sheppard almost did. Assassinations were the usual programming, but what happened here wouldn't be out of the question. These guys would do whatever they were programmed to do then blow their own heads off."

"Do you think these Goa'uld turned John into a…za'tarc?" Teyla slowly pronounced the unfamiliar words.

"Not the Goa'uld." McKay looked at Elizabeth. "The Trust, however, would certainly try."

The room fell silent. They were all thinking about what happened with Col. Caldwell. After several seconds, Elizabeth turned to Lorne.

"Major, I want you to go to the SGC and talk to Gen. Landry. You can tell him what happened here, but no-one else. I want whoever is behind this to think nothing has happened yet. We have to find out who Col. Sheppard was with and what they did to him." She looked around the table. "I'll write a note for you to give to the General while you get ready. We'll have to come up with a good cover reason for you to be there."

Lorne nodded and stood up. "Yes, Ma'am. How about we found some intel on the Wraith weakness?"

"That'll work. It's a good reason to have someone go the SGC in person." She looked at the others. "We also need to find out if anyone else in Atlantis has been affected."

"We can scan the city for any unauthorized transmissions." Zelenka offered.

Beckett also stood up. "We'll start screening everyone for this drug."

McKay snapped his fingers at Lorne. "See if you can bring back a za'tarc detector. Talk to Col. Carter about it. You can tell her what's going on. If you need a cover story for anyone else, uh, you can say we need it to get more information from Wraith worshipers that gave us the intel. We need to know if they're telling the truth."

Elizabeth winced. "That's a bit slim, Rodney."

"I said if he needs to."

"Okay. Let's go." Elizabeth was relieved there was something to do. She could see that relief in the others as they filed out.

Beckett, however, hung back.

"What is it, Carson?"

"John wants to see you."

She nodded and started to walk out but paused. "You said he's going through withdrawal. How bad is it?"

"So far, he's experiencing muscle tremors, a severe headache, sweating and nausea. It's not as bad as Rodney's withdrawal from the enzyme, but it is serious with the injury. He refuses to let me give him anything to help. He just says that he doesn't want any more drugs. And, he's not talking, but I know he's very distressed about all this."

"As horrified as I am about how close John came to destroying this place, I can't imagine how he's feeling."

----------

Elizabeth put on what she hoped was an encouraging smile as she and Beckett entered the room. Sheppard was the only patient in this area. It was necessary for privacy as well as security. The head of the bed was raised just enough for him to be able to see around the room without having to move. The long incision across the right side of his abdomen made use of the muscles there nearly impossible and extremely painful.

He now wore white scrubs, the heart monitor leads snaking out from the neck. He stared blankly at the foot of the bed. They could see the pain from the wound and the withdrawal were etched into his face. He did not seem to notice their presence.

"You need to send me back to Earth." The flat statement threw them off. Sheppard did not make eye contact, more by apparent introspection than actual avoidance.

"What?" Beckett responded first.

"We don't believe you did this willingly, John." Elizabeth tried to convince him. She was certain of the statement, deep down inside, she knew it to be true. She was still frightened, though. The conversation in the conference room left her with the thought that John Sheppard might still be under the influence of the Trust. That thought nagged at all of their minds. "We think the Trust is behind it. Evan is on his way back to the SGC to talk to Gen. Landry. I hope he can…"

"You can't risk it. You have to send me back to Earth." He repeated. They could see the effort it took for him to say it.

"No, I do not. We think we have a good idea of what happened and Evan will turn up something."

He finally looked up at her, but just long enough for her to see his eyes were filled with despair. "You can't take the chance I'll do it again."

"I'm not taking any chances." Elizabeth held his gaze. "Dr. Beckett will have someone with you at all times, and we've posted two Marines right outside your door. I really don't think you're in any condition to get by them."

Sheppard looked down and the inward stare appeared again. "I'm kinda tired."

She looked at Beckett, who nodded with a trouble frown. "Okay. We'll let you get some rest. I'll be back later."

A nurse entered as they left.

Teyla was waiting for them in his office. She could see their dismay.

"How is he?"

Elizabeth exhaled slowly. "John wants me to send him back to Earth."

"You're not going to, are you?" Beckett asked quickly.

Elizabeth shook her head just as quickly. She was genuinely shocked at the thought of it. "No! God knows what they would do to him."

"Good, I was thinking the same thing."

"What can we do to help?" Teyla asked.

"Give him time. It's not going to be easy. These drugs are messing with his head as well as his body. Until it is out of his system, John won't be thinking straight, as much as is trying to. He has to come to grips with whatever it was that happened on Earth and what he did here. It's going to take time and the support of his friends."

"We will do everything we can to help."

----------

Quiet voices drifted in. Sheppard opened his eyes to see Ronon sitting on a nearby chair, talking quietly with Jennifer Keller. He closed his eyes again. The 36 hours since he first regained consciousness after surgery were a blur. The headache persisted almost unabated. The rest of his body didn't feel much better, but it was better than …earlier. He vaguely remembered telling Elizabeth to send him to Earth and she said he wasn't responsible. Responsible? Responsible for what?

"Jesus!" Sheppard struggled to sit up. He looked at Ronon. "ZPM. Gotta stop it."

"Sheppard!" Ronon sprang out of the chair and rushed over.

Jennifer beat him to the bedside. They both restrained Sheppard and gently pushed him back down.

"Colonel, please, you can't get up."

"Relax. The ZPM isn't going to explode." Ronon looked at him with a worried expression.

Sheppard stared at each of them for a long time before he realized things were alright. He relaxed, then deeply regretted trying to get up, especially since it seemed didn't needed to. It felt like someone hit his head. Hard. His stomach heaved into his throat, and he convulsively swallowed the bitter bile.

"Help me roll him on his side." The young doctor instructed Ronon. They quickly turned him onto his left side. She grabbed a kidney dish from the bedside table and held it near his mouth. "Get Dr. Beckett for me please."

He nodded and ran out.

"Slow, deep breaths, Colonel. It'll pass." She could feel cold sweat moisten the scrubs he wore.

After a couple of seconds, he swallowed again. "Water?"

"Water? Let's wait a bit, okay?"

"Please." He could barely manage a whisper.

The young doctor repeated as she set the dish next to his pillow. She quickly scanned the heart monitor, pulse oximeter and the IV. Her voice was soft and light but got through the pain and receding nausea. "Okay. Just a sip, though."

"Just a sip, then." She poured a little water into a glass and held the straw to Sheppard's mouth. He let the cool liquid wash through his mouth and trickle down his burning throat. She allowed him a couple of small sips then put the glass on the table. "I think that's enough for now, Colonel. How are you feeling?"

He turned his head enough to look at her, squinting even in the dim light. "Head hurts."

"What happened?" Beckett hurried in and came around to stand next to her. Ronon stopped at the end of the bed.

"He thought the ZPM was going to explode and tried to get up again," Ronon said

"How is he?"

"Col. Sheppard was disoriented again when he woke and became nauseous when he tried to get up. He still has a severe headache with sensitivity to light, Dr. Beckett." Jennifer glanced at the heart monitor. The rate had spiked but was returning to normal. "Same as before."

Ronon stared at Sheppard, his arms folded over his chest. His expression was dark with worry. "When is it going to stop?"

"Soon, I hope." Beckett compressed his lips as he picked up Sheppard's chart and began to read it. "The drug is being broken down in his…"

Sheppard cleared his throat. The fog in his mind didn't seem to want to clear today. "What drug? What the hell's goin' on?"

"You were drugged while you were on Earth, John. The withdrawal is causing the confusion you are experiencing." Beckett explained patiently. He was more than a little concerned. This was the fifth time he'd explained it. He could see Sheppard was beginning to remember they were out of danger.

"The ZPM?" Putting it together was slow and painful. "You sure?"

"Yes. It's safe. McKay's checked it out." Ronon answered. "He said all the important systems are back online and functioning normally."

Sheppard briefly turned his head to look at him. He frowned, wanting to believe him. "Elizabeth? She's okay?"

"She's fine, John. You were talking to her a few hours ago." Beckett smiled at him.

"…time is it?"

Beckett checked his watch and cursed to himself that he still had to convert to military time. "Uh, about 1400 hours. It's been about a day and a half since you were shot."

Sheppard took a moment to absorb that. The tight bands squeezing his head since he first woke had eased only a fraction, still making it difficult to think straight. Amongst the jumble, though, there was one thought he remembered clearly. "Have to send me back to Earth."

"Just forget that kind of talk. You're staying right here." Beckett waited until Sheppard exhaled heavily and nodded. "Now, would you like something for the headache?"

"No. No more drugs." His voice broke. He tried to clear his throat again. "S'more water?"

"Just a little."


	4. Chapter 4

Beckett was only half surprised to see the trio waiting as he came out of surgery. "He's fine."

"I still don't get why you had to cut him open again." Ronon growled at the doctor.

"Well, because the liver…"

"Do we have to go over it again?" McKay grimaced at the thought of listened to the details one more time.

Teyla asked. "He will be alright?"

"Aye, physically, I believe so." The doctor held his hand up to stop their questions. "Until we hear from Maj. Lorne and the drug is completely out of his system, I don't know any more than that. He's in recovery right now. You can come back and see him later."

"Thank you, Carson." Teyla nodded and smiled. "I will let Elizabeth know."

----------

"Any news from Maj. Lorne?" McKay stood in the doorway to Elizabeth's office, a deep frown creasing his brow.

She lowered the lid to her laptop as she looked up. "No, Rodney. It's barely been three days. I think it will take at least a week to get any news, if at all."

He came into the room and sat down. He spoke quietly. "You think they'll be able to find out what happened?"

"I don't know." She sighed and sat back. "I know very little about the Trust, but what I do know is frightening enough. If they find out that John did not destroy the city and Gen. Landry is investigating, the people that did this will probably just disappear."

"Do you think Sheppard will…"

"I don't know, Rodney." She knew what he was going to ask. He'd already asked it, and more than once. She only hoped that they would be able to help Sheppard get past this, to heal. "So, everything is back to normal?"

McKay was startled out of his thoughts by the change in topic. "Uh, yeah, I think so. Well, we're running a few more simulations and tests, but the major systems are good. We have everything we need for security and day to day running of the city."

----------

The lights were dim when Elizabeth entered the infirmary room. She walked over to the nurse who was busily working on a computer. "Can I have a few minutes, please?"

The young man nodded and quietly stepped out of the room.

She paused to see if Sheppard would acknowledge her. He didn't. The head of the bed was raised so that he was almost sitting upright. Beckett told her his mind was clear enough to understand and follow what was going on around him and he no longer woke up thinking that the city was about to be destroyed. The doctor also said that he was withdrawn. While it was understandable, it was worrisome.

"Hey." Elizabeth smiled as she approached the bed. She tried to keep her tone neutral, not serious, but not too light. "Carson said you were awake. How are you feeling?"

"Fine."

"John." She felt the muscles tense when she put he hand on his arm. "It wasn't your fault."

"How do you know? There's no proof."

"Maj. Lorne will find something." She hoped, even prayed, that he would. Otherwise, her friend would go back to Earth and be tried for treason and the attempted murder of hundreds. He would be convicted, but he'd probably plead guilty to get it over with, she thought bitterly. It would mean a death sentence, one that would be carried out quickly and quietly.

He looked up at her just long enough for her to see the same darkness she saw earlier. "Elizabeth, just...just…drop it."

"Alright." She tried to think of something to talk about. "Uh. You should know that Rodney has given the city a…"

Sheppard closed his eyes and shook his head. "Look, I'm kinda tired. Do you mind?"

"Okay, you get some rest. We can talk later." She feared he'd do this, but didn't want to press him. As she left the room, Elizabeth glanced back to see him staring at nothing. She fervently hoped that Lorne would find the evidence needed to clear him.

As Elizabeth left, the nurse returned to his chair. He watched the patient for a moment then began working again.

Sheppard closed his eyes, but didn't sleep. He tried once more to recreate the trip to Earth. Start at the beginning, no, the prologue. The orders. As it often happened in the military, especially the top secret military, the orders were vague. 'Report to the SGC for debriefing.'

Gen. Landry couldn't elaborate beyond the belief that he was wanted to go over some mission reports, check out what could be some Ancient technology and discuss tactics. No, the general would not be at the meetings. He had his hands full at the SGC right now.

Rodney had been well and truly pissed that he wasn't asked to go back. Sheppard would have been more than happy to change places at the time. The brass didn't really approve of him, and he didn't much care for them.

He rubbed his forehead to ease the tension. First came the orders. Six hours later, he flew the Jumper through the Gate bridge and into the SGC. There was a quick debrief with Landry then a couple of guys, not Marines, drove him out to the airfield. This was where it got fuzzy. He was certain they boarded a small transport jet. What was it? He should know what kind of plane it was. He tried to picture it, but he could only recall it was non-military and small.

Sheppard couldn't quite get past this point in the chain of events. Everything after seeing the plane on the tarmac was blurred, not really a memory. It was like something seen out of the corner of the eye. By the time you turn to look, it's gone, leaving only an impression.

When Elizabeth and the others asked how the trip was, he only responded that it was long and boring. She accepted that and dropped the subject. Only, he didn't remember long and boring or anything.

The throbbing that nagged at his temples was spreading again.

Beckett came in with a very large male nurse. They both had their best bedside faces on, cheery smiles and exuding all the confidence in the world.

"Colonel, let's take a look at the incision, then I think it's time we get you out of bed for a few minutes."

Inwardly, Sheppard groaned. He just wanted to be left alone.

----------

The room was quiet and the lights low. Sheppard sat in one of the chairs meant for recuperating patients. It was comfortable and could partially recline. Kate Heightmeyer sat nearby, otherwise, they were alone. She had seen him the day before, but was still concerned with his appearance. Instead of improving, he looked even more ill. Beckett told her Sheppard had no appetite and wasn't able to keep food down. He didn't expect that to change for at least another day or so. This was making his recovery even more difficult.

"Colonel, it's still too soon to know if the memory loss is permanent." She studied his face closely and could see that it was eating at him. Losing control was not something that ever sat well with Sheppard, but this situation was a nightmare. "Once we understand what the drugs are and what happened on Earth, we may be able to reconstruct your memory and fill in at least some of the blanks."

He looked at her. "It's all a blank. From the time I saw the plane until I was in the Gate room, trying to destroy the city, I don't remember anything more than a few…few faces and maybe rooms. And, even those are fuzzy. I don't even know if any of it is real."

"What about how you felt? Do you remember feeling well, sick, any pain?"

Sheppard's eyes clouded and his right hand involuntarily went to his head and rubbed the temple. She remained silent as he thought. Kate did not want to interrupt anything that might be coalescing in his mind.

"Needles. Injections. I don't know what or why. I was tired. I know I wanted to sleep, but," he licked his lips and looked away, "I couldn't. Headaches. Bad ones. It was like the last couple of days, but worse. If that's possible."

"What about the pills? Do you remember why you were taking them?"

He frowned, looking inwardly again. After a moment, he shook his head slowly. "I think they were for a throat infection, but..."

"You don't remember being sick?"

Sheppard shook his head once. When he spoke again, his voice was strained. "What the hell happened to me?"

"I don't know, John. We may learn more when Maj. Lorne returns."

He rubbed his face wearily with both hands then exhaled heavily. "Yeah, maybe."

----------

"What if Lorne doesn't find anything?" Ronon asked what they all feared. He stood in the door of Elizabeth's office, looking around at her, Teyla and McKay.

McKay went one step further. "What if there's nothing to find?"

Elizabeth and Teyla glared at him, while Ronon's frown just deepened.

"Rodney, how can you even think it?"

The astrophysicist shifted uncomfortably in his chair. He spoke weakly. "Well, it's something we should consider. He's been gone nearly six days."

The familiar sound of the Gate activating and the announcement of an incoming wormhole sent them hurrying out to the ops area.

"Are any teams scheduled to return?" Elizabeth asked Chuck.

"No, Ma'am." He shook his head.

McKay pushed another technician away from a computer and quickly read the screen. "Lower the shield, it's Lorne. About time, too."

Moments later, a Puddle Jumper emerged from the event horizon and rose to the Jumper bay.

-----------

Teyla, McKay, Beckett, Lorne and Ronon followed Elizabeth into the conference room. They all needed to know what had been discovered.

Lorne looked tired as he waited for the conference room doors to close. Once they had privacy, he handed Elizabeth a flash drive. His face was composed, but she could see deep anger in his eyes. "Everything found so far is all there, Dr. Weir."

"Did you bring back the za'tarc detector?" McKay asked.

"Yes, but Col. Carter and Dr. Lam didn't think it would be much help. Something about the way the drugs probably affected the Colonel's memory." He shrugged. "We also found files that talk about the drugs they used."

Beckett swore under his breath. "What were they?"

"I don't understand that stuff, Doc, but they used multiple drugs, and other…means to condition the subjects." Lorne looked a little unwell. He pointed at the drive. "Dr. Lam said it looked like we got all the research materials."

"Have you read it?" She asked as she set it on the table. They all stared at it, needing to know the contents, but not wanting to know the details.

"Just enough to know that I wouldn't wish what they did to Col. Sheppard, and a lot of other people, on my worst enemy." Lorne's carefully composed expression could not hide his anger and disgust. "We found dozens of case files and research materials going back six or seven years. The SGC, Agent Barrett and some other guys from the NID are going through them and tracking down the…subjects."

One door suddenly swung open to reveal Sheppard leaning on a burly young Marine. He was dressed in white infirmary scrubs and a dark blue robe. Stubble several days old darkened his cheeks and he blinked in the bright light. A very upset nurse followed closely, protesting his being there. Another Marine was behind her.

"Colonel, you need to come back to the infirmary." She looked at Beckett as he got up and hurried around the table. "I'm sorry, Dr. Beckett. He insisted on coming here."

The Marines looked decidedly uncomfortable as Sheppard motioned to a chair.

"Colonel, just what do you think you're doing?" Beckett pulled the chair out for him.

"Sergeant?" Lorne said menacingly, obviously not happy with his men.

"My fault." The colonel said as he eased into the chair.

"John…" Elizabeth started.

"I'm fine." Sheppard was very pale and unsteady, but they could see his determination. He felt more than saw them staring.

"No, you're not fine." Beckett exhaled heavily then nodded. He turned to the nurse and Marines. "It's okay."

Sheppard nodded at the young men. "Thanks, Sergeant. Wait outside."

"Yes, Sir." They backed out and the door closed again.

Beckett returned to his chair nearby. He turned slightly so that he could watch Sheppard closely.

Lorne glanced at Elizabeth, who nodded. "Sir, I was just telling them the guys that had you have done this to at least several dozen others."

"Ken Richardson was among them?" Beckett asked this.

"Yeah. He was a little different, though. The Trust recruited him a year or so ago and were able to get him into the Stargate program as a mole. He sat tight, went to work everyday and did nothing to give himself away. When the plot with Col. Caldwell failed, they seconded Richardson for training," Lorne crooked his fingers into quotation marks, "and gave him a crash course in self-sacrifice. Once they were able to set up getting the Colonel back to Earth, they arranged his assignment here. Richardson was needed here to make sure Col. Sheppard blew up the city."

They all looked at Sheppard. Lorne winced. "Sorry, Sir."

"Go on." The colonel dismissed the apology with a bare wave of one hand, but they could all see it troubled him. He leaned forward slightly, propping his elbows on the table and curling his right hand over the left. Avoiding the sealed IV set-up still attached to the back of his hand, he rested his chin on his fingers.

"At least we can prove you weren't responsible for your actions, John." Elizabeth said as she pushed the flash drive to Beckett who connected it to the data pad he carried in. As he skimmed through the data, the doctor's expression changed from rigidly neutral to shock to anger.

"Dear God." He swallowed hard. "What the hell were they thinking?"

"What? What does it say?" McKay demanded.

"Carson, I'd like you to go through the file and summarize it, please." Elizabeth asked, not wanting all of the details read out just yet.

"Yes, of course, there's a lot of data here." Beckett could not hide his shock and anger. He quickly looked at Sheppard as he saved the data to his pad and gave the drive back to her.

"What has happened to the people that did this?" Teyla asked as she tore her eyes from the tiny storage unit to look up at Lorne.

"How did you find them?" McKay strained to see the file on Beckett's pad then looked at Lorne.

"It was surprisingly easy. They were hiding in plain site. The NID figured these guys set up shop somewhere in Area 51. It was just a matter of where. I guess they thought that once the city was gone no one would ever know what happened."

"And, no one would go looking for them." Elizabeth shook her head. "Who are they?"

The major sighed and shook his head. "Hard to say. The head doctor was a guy called Eric Coleman…"

Beckett gaped at Lorne. "Wait, I know him! Tall, thin man with a slight limp?"

"Don't know about the limp, Doc. He was dead when I saw him, but he was tall and thin. He overdosed on some of the stuff they gave to Col. Sheppard. There's evidence that it may not have been his choice. Sorry." Lorne raised his hands in apology. "We think there're some brass involved, as well as politicians and more than a few civil servants and corporate types. Isolating the location and protecting it from the rest of the base is no small feat."

"Excuse me? Didn't anyone know what the hell they were up to?" Beckett demanded indignantly.

McKay answered with disgust. "Not necessarily. Everything is top secret. I was there for several weeks and saw almost nothing outside of my own lab. There are different security clearances for each building, and sometimes for the floors in a given building. It's extremely paranoid, so you don't go nosing around."

"That's true." Lorne continued, looking at his CO. "Since that's where you were supposed to be anyway, Sir, it was probably safer to keep you there. You were in meetings or testing Ancient technology if anyone asked. The project was housed in a small building on its own. They had their own security and staff, which isn't unusual for some of the projects there."

"Did you find others there that have been…?" Sheppard asked quietly. "What happened to them?"

"We found four more people undergoing the…treatment at the facility, Sir. They're in the hospital now. The NID and SGC are tracking down all the rest, at least the ones we found files on. We think there's more than a hundred."

"They don't know how many?" McKay was alarmed.

Lorne shrugged. "Not yet. The experts are digging through all of the computers and searching for any indication of more. They said it could be weeks before they know, if then."

"Does that mean there could be someone else on Atlantis that might attempt to destroy the city?" Teyla asked.

Lorne shook his head. "It's unlikely. They would have made their move before now. The conditioning is effective for a finite amount of time."

"How long?" Beckett started skimming through the data on the pad again.

"Sorry, I'm not sure. The doctors at the SGC only just started going through the files when I came back. We do know, though, that the drug Col. Sheppard was taking is necessary to keep unwilling participants under control. If they stop taking the drug…"

"Withdrawal starts." McKay interrupted the major.

"They recently finished testing implants that slowly releases the drug over about three months, and were working on longer lasting implants. Now these guys had access to all of our reports, so they knew everyone coming from Earth is scanned for Goa'uld."

Beckett finished the thought, "And, that any implant would be found."

"Right."

"Why didn't Sheppard do it the first night?" Ronon asked.

"Richardson needed to be on duty in the Gate Room. He had to pick a time when there was minimal activity. Depending on returning missions or whatever, there can be any number of people in the vicinity." Lorne answered. "They were worried that if the city was destroyed immediately, there would have been suspicion that the two might be connected, and that the Trust was involved again."

Everyone at the table surreptitiously watched Sheppard throughout the conversation. He stared at Beckett's data pad, seemingly unaware of their attention. His eyes gave away nothing, but McKay sat close enough to see the muscle in his jaw jumping with tension. He caught Elizabeth's attention and tilted his head toward Sheppard. She immediately understood.

"Thank you, Major. I think we should let Dr. Beckett read and assess the files. Carson?" She raised an eyebrow at the doctor and pushed her chair back.

"Yes. I'll have a preliminary report for you by morning." He stood and picked up the data pad then looked at Sheppard. "And, you, Col. Sheppard, are going back the infirmary."

Sheppard glanced at Beckett then returned his gaze to the data pad. "I want to read it."

"John." Elizabeth stood up.

Sheppard ignored her. It was as if he could see only the computer.

"Is that a good idea? To let him read that, I mean." McKay was looking from Sheppard to Beckett to Elizabeth and back at Sheppard.

"Colonel, I think we should talk about this later. I want to you get some rest." The doctor focused on his patient.

The little color he had upon arriving had completely drained from Sheppard's face. He licked dry lips and swallowed. "I have to read it."

Everyone was frozen, watching him. Elizabeth thought of the single-mindedness that he displayed a few nights ago. His voice and the look in his eyes were the same. There was an intensity that chilled her.

"John, we'll talk about it later. Come back to the infirmary." The doors swung open as Beckett approached Sheppard. "Come on, son."

Ronon got up and walked around the table to stand next him. The flurry of movement seemed to break the hold the data pad had over him. He nodded and pushed the chair back, wincing with the effort. Ronon waved the Marines back and helped him up.

"I'm okay!" Sheppard tried to pull away, but Ronon ignored him. The Satedan hooked his arm under Sheppard's and slowly turned both of them to leave.

"No, you're not. Let's get you back to bed." Beckett gently grasped his other arm. The two Marines fell in behind them. Elizabeth, McKay, Teyla and Lorne remained in the conference room, watching the little procession leave.

"Elizabeth?" Teyla had seen the shock on her friend's face. "Are you alright?"

She inhaled sharply and looked at her young friend. "Yes, yes, of course."

"Is Beckett really going to let him read that file?" McKay asked, still staring in the direction Sheppard and his escort went. "I don't think that's a good idea."

"Dr. McKay may be right, Dr. Weir. From the little I've seen and heard, they did a real number on Col. Sheppard." Lorne agreed. The others looked at him. "I didn't want to say much with him there, but it must have been a very long nightmare. Like I said, I don't understand a lot of it, but they really messed with their victims' heads."

"What happened to the people that completed their assignments?" Teyla asked, already suspecting the answer.

The major's discomfort increased. "There are no survivors in this program. They all either died during conditioning, while they were completing their tasks or killed themselves afterwards."

"Like Richardson." McKay observed flatly.

"Yeah, like Richardson."

"Well, perhaps because John survived and stopped the overload, he is no longer in danger." Teyla suggested hopefully.

"As long as he doesn't get the urge to finish what he was supposed to do." McKay said morosely.

"Rodney!" Elizabeth admonished him with her tone.

"Well, it's something we need to keep in mind."

"I'm sure we're all aware of that, including John."

----------

"Into bed. Now." Beckett released Sheppard's arm and pointed at the bed as they entered his infirmary room. "Ronon, would you help my errant patient back into bed, please?"

"Sure." Ronon nodded and, with the nurse's help, removed the robe and gently settled him into bed.

Sheppard was silent throughout the journey back to infirmary. He was grateful for the transporters making it quick and relatively effortless. Even so, the energy he expended on getting to the conference room drained him. Beckett warned him that the effects of the withdrawal and what happened on Earth would probably make his recovery from the wound significantly slower than normal. Tiring quickly was to be expected until his body was clear of the drugs and he was able to get some proper nourishment. The intravenous nutrients he was receiving weren't enough. The wound itself had consequences, too.

He barely followed Lorne's narrative. The persistent headache still made concentration difficult. It had eased, but not much. His entire being focused on the flash drive and the data it contained. The few memories he had of those days on Earth were vague at best, and quite possibly false. He ached to know more, to know everything.

"Okay, I think you've had enough excitement for one day." Beckett caught Ronon's attention and inclined his head toward the door.

The Satedan nodded and looked at Sheppard. He could see weariness in his friend's eyes. "I'll see you later."

"Yeah, thanks." Sheppard lay back and closed his eyes as Beckett and the nurse reattached monitor leads and got the IV going again.

"Let's see if you've caused any damage." Beckett carefully moved the scrub top and the dressing. He closely examined the healing wound. The peritoneum and muscles were surgically closed, but there were no external stitches. He was allowing the dermis and epidermis to heal slowly, hopefully resulting in less scarring. It was doing just that. Satisfied the excursion had no visible effects he applied a new dressing and straightened the top again.

"Do you want something for the headache?" The doctor's voice was quiet.

"No. It's not bad." He shook his head once and opened his eyes briefly.

"Liar." Beckett said under his breath as Sheppard's eyes closed and breathing slow. "Sleep well."

As Beckett turned to leave, Sheppard's voice stopped him. "Carson, I want to read it."

"I know, son. Let me go through it first then we'll talk about it. Okay?"

"'Kay."

The doctor stood and watched his friend for two or three minutes. After making sure he was asleep, Beckett picked up the data pad and walked out.

----------

Beckett stopped at the door to his office and looked down at the data pad. He sighed. It was not a good idea to read the files where he could be interrupted, or where he couldn't swear. Both were distinct possibilities, no, probabilities. He turned and headed back to Sheppard's room. The Marine detail still stood guard outside. He beckoned the duty nurse over.

"Is something wrong, Dr. Beckett?" She asked, concerned at seeing him back so quickly.

"No, I just wanted to let you know that I'm going to get a sandwich then I'll be in my quarters for a while. Dr. Cole is on duty and Dr. Keller is on call."

She smiled. "We'll call you if anything comes up."

He looked at the Marines. "Please don't let Col. Sheppard leave again without a doctor's express permission."

"No, Sir." The sergeant cringed inwardly. "Sorry, Sir."

Beckett shook his head, understanding the young man's position. "Don't worry about it. I know how determined Col. Sheppard can be."

"Thank you, Sir." He replied, grateful for the acknowledgement, but was still kicking himself as the doctor walked away.

Beckett entered his quarters a few minutes later, data pad under one arm, sandwich and coffee in his hands. He opened the sandwich and took a bite before sitting down. He was hungry now and had a distinct impression the files on the pad would ruin his appetite. As he ate, Beckett connected the pad to his laptop so that he could read from the larger screen.

Finally, he settled into the chair and exhaled heavily as he opened the first file.


	5. Chapter 5

"How are you feeling this morning?" Beckett asked as he entered the infirmary room, eyes down scanning the overnight entries in the chart. He looked up to see Sheppard standing next to the bed. He was rolling his IV stand next to the reclining chair.

Sheppard replied. "Better than you look."

"Is the headache any better?" He peered closely at his patient and had to agree that he appeared to be greatly improved. His eyes were clearer and his whole body was more relaxed.

"Yeah, a lot better." He sat down.

"I hear you had a good night's sleep. Hungry?" Beckett asked hopefully. Nausea from the pain and drug withdrawal all made eating impossible.

"Sorta. It looks like you didn't get any sleep at all." Sheppard tried to get comfortable but finally gave up. The six-inch incision just below his ribs still felt like a six-inch incision, and the doctor had been digging around in there. Twice. It was going to take a little more time to be really comfortable again.

Beckett pulled up another chair and held up the data pad as he sat down. "Not much. I spent the night going over the files Maj. Lorne brought back."

"Are you going to let me read it?" Sheppard already knew the answer.

"No." Beckett held up a hand to forestall any protest. "Wait. I haven't finished going through everything, but there's just far too much medical jargon and most of it would mean little or nothing to you. I'll tell you what's in here and what it means. Okay?"

He thought for a moment then nodded, but before the doctor could begin, one of the nurses walked in with a tray.

She stopped when she realized she was interrupting them. "I'm sorry, Doctor."

He waved off her apology. "That's alright. I want Col. Sheppard to eat something."

She set the tray on a low, wheeled table and moved it next to Sheppard. "Okay, Sir. I brought juice, toast and a small bowl of fruit. I'm sure Dr. Beckett won't mind making sure you eat it all."

"I'll be sure he does. Thank you, Patty." He smiled at her as she left then looked at Sheppard and pointed at the tray. "Like right now."

Sheppard sighed and began to eat. After downing half the toast and juice, he looked expectantly at Beckett. "Well?"

The doctor ignored him, looking at his chart. He wanted his patient to eat everything before talking about the contents of the file. "First things first. The incision is healing well now, and your liver function is improving. I think you'll be happy to know that your system is nearly clear of all of the drugs you were given while on Earth."

"Long term side effects?" Sheppard asked as he picked at the fruit. He finally speared a piece and put it in his mouth. He wasn't really enjoying it, but knew Beckett would not be satisfied until it was gone.

"The difficult withdrawal is noted here, but it will take a little time to know for sure if there'll be any long term effects or what they might be." Beckett had to concede. They wouldn't know for months or years, if then. The data in the files Lorne brought back went back only seven years, and use on humans just five. Many of the victims were still being tracked down or were hospitalized. The rest were dead.

"How many? How many people did they do this to?"

"According to the files, it looks like it was about a hundred, including the original test subjects."

"Guinea pigs." Sheppard ate the last of the fruit and put the bowl back on the tray. His eyes were clouded and hard to read.

"Yes, well, they're being rounded up so that they can be cared for."

The colonel snorted bitterly. "So they won't blow anything up, you mean."

"John…"

"What happened?" Sheppard was tired of waiting. He knew Beckett was hesitant to talk about this, but he was determined. "What the hell did they do to me?"

Beckett glanced down at the data pad, but he didn't need it. He switched it off and set it aside. Writing the report for Elizabeth, even just reading the files, had burned the details into his memory. He didn't need reminding about any part of it.

"You said your last memory was seeing the plane, right?"

"Yeah, but I don't even remember what it was."

"Well, I'm not surprised. The file is remarkably detailed. Dr. Coleman was obsessive in that respect." Beckett took a deep breath. "The men with you used one of those Goa-uld zat guns on you. They started giving you the drugs as soon as they had you on the plane."

"What kind of drugs?"

"It was a cocktail more or less designed to..." He paused. "Let me go back and tell you what the overall process was."

Sheppard only nodded.

"Coleman used a combination of drugs and sleep deprivation to breakdown the defenses of the victims as quickly as possible. Sleep is essential to create memories, by the way. That may be one of the reasons you are having difficulty remembering anything."

"Will any of it come back?"

"To be perfectly honest, it's hard to say. Two of the drugs they used on you are completely unknown and probably created for this purpose." He frowned, thinking. "Or, they may have been created for legitimate purposes, but never made it past trials. They may have found adverse side effects and…We might be able to track down the drug company that made them."

Sheppard cleared his throat.

"Oh, sorry. Anyway, the combination of these drugs and the effects of sleep deprivation may have sufficiently interrupted the normal process of laying down memories that there is little or nothing there for you to remember…" his voice trailed off. "I'm sorry, John."

"Okay. Go on." Sheppard nodded, but gave no sign of what he was thinking.

"Of course. Well, the first couple of days in the process were spent increasing the dosage of the various drugs until they reached optimum levels and efficacy. During this time, they used subliminal methods to program ideas and instructions into the mind of the subject. Once a certain state was attained, the conditioning was intensified, using both overt and subliminal methods.

"Normally, the whole process required at least eight days. According to Coleman, you were his most difficult subject. He was worried that eight days was not sufficient to guarantee the programming would work, so he intensified the process with you." Beckett stopped.

He'd been condensing the events to the point of making it an impersonal executive summary. It was difficult to think about what these men did to his friend, or to any human being, unless he put it in a clinical perspective. He worried about how the man sitting before him was taking it.

Sheppard sat without moving or expression. His arms rested lightly on the arms of the chair, hands hanging limply and unmoving. It was as if he didn't even hear what the doctor was saying. They could have been talking bout the weather for all the emotion he was showing. The lack of expression or movement worried Beckett. Sheppard was almost always in motion, and his face, or his eyes, reflected what he was thinking more often than not.

Again, there was just a nod. "Go on."

"Coleman pushed the process to ensure your cooperation. He gave you dangerously high doses of the drugs and increased them more rapidly than is advisable." Beckett watched Sheppard closely. "They increased the dosage too fast. It caused ventricular tachycardia. That's where the heart beats much too rapidly. They had to use a defibrillator to shock your heart back into normal rhythm.

The only visible reaction was a momentary frown.

Beckett took a deep breath and continued. "The incident didn't stop them. Coleman slowed the increase in the dosage just enough to avoid repeating it. According to the file, the concentration levels he needed for you were reached after five days. That's when they let you sleep for the first time. And, that's when they started the programming in earnest."

"Oh, good, you're up." McKay hurried in, laptop cradled in one arm. He barely slowed when Beckett turned in his chair. "I figured it out."

"Rodney!" Elizabeth followed a second later. She stopped when she saw that Beckett and Sheppard must have been talking. From the look on the doctor's face, it was serious. "I'm sorry, John, Carson. We can talk about this later, Rodney."

"No. Stay." It was Sheppard that spoke. "You need to know this anyway."

Elizabeth blushed guiltily. "Well, I read Carson's report this morning."

"Uh, me, too." McKay admitted reluctantly.

Beckett gaped at the astrophysicist. "How the hell did you get…?"

"You know I can hack any computer in two galaxies." He was only mildly repentant. "Besides, I needed to know what happened. I haven't been able to crack the code yet. I thought it might help to know what they did."

"It doesn't matter." Sheppard dismissed the doctor's concern. "Go on."

"Where were you? McKay asked.

"Just sit down and listen." Beckett was unhappy with the interruption but tried to maintain an outwardly even tone.

"Yes, yes. Of course." He perched on the bed as Elizabeth sat a nearby chair.

Beckett waited for them to settle before he took up the story again.

"Coleman played a prerecorded scenario while you were asleep. They were building a story, a history of false events, in your mind." He slowed the narrative a little. He was hoping for some kind of recognition or reaction from his friend, but again, there was nothing. "Well, uh, for the remainder of the time you were there, Coleman and his people continued to play the recording to you whenever you slept. When you were awake, they acted out the scenario."

"What was it?"

"It was the…" McKay started.

"Rodney, let Carson tell it." Elizabeth stopped him. Her expression indicated that he should stay quiet and he saw it.

"Uh, sorry. Carry on."

"It was an invasion of Atlantis by the Wraith. They worked on it for some time. Everyone that had contact with you played a part. They had scripts, radio transmissions, everything necessary to sell it.

"Anyway, the story was that the Wraith were able to gain access to the city through their human worshippers infiltrating by saying they were survivors of a culling. Most of the expedition was either dead or taken prisoner. Some were compromised and under Wraith influence. The self destruct was disabled. You were the only one left that could keep the Wraith from using the Gate or the city to get to Earth. They also worked in that anyone in the Gate room at the time would be under the influence of the Wraith."

"So I believed that Elizabeth…?"

Aye, or any of us." The doctor paused again. "Do you remember any of this?"

"No." Sheppard replied with hesitation. The tiny frown crossed quickly his face again. "Why don't I?"

"I don't know." Beckett frowned and picked up the data pad. "I didn't see anything in the files that would account for an absolute lack of memory. It may be a side effect of the drugs."

"They didn't expect you to survive the mission, John." Elizabeth offered. "Anyway, it would be better for them if you had no memory. You would have no defense whatsoever if it didn't work."

"No, I wouldn't." Sheppard said flatly. They all fell silent for a moment.

"Was there anything in the files about a code? What it was used for?" McKay demanded.

"Code? What code?" Sheppard asked, eyes narrowed.

The astrophysicist pointed to his ear. "Your transceiver had a second receiver. It was getting a signal similar to Morse code that was transmitted from Richardson's quarters. You know, the technician that shot you then killed himself. Well, he was one of them."

"The Trust sent him here to make sure you completed the mission they set you on." Elizabeth explained. "They were worried that you might do precisely what you did, reverse the overload."

Sheppard stared at the floor, thinking. After several seconds, he looked at Beckett again. "Did I tell them anything?"

"No, I don't think they asked you anything. The NID and SGC's initial analysis indicates that they only wanted you to destroy the city."

Elizabeth added, "We put just about everything in our reports. It seems the Trust has been able to gain access to every bit of information we send to Earth. They didn't need to ask you anything."

There was another long pause as he absorbed their responses. Each time, he stared at the floor, deep in thought. He looked up again. "Why did I stop the ZPM exploding?"

Now it was Beckett's turn to think. "I believe it was a combination of things, John. The trauma of the gunshot, as well as the difficulties Coleman had in conditioning you and the fact that you had essentially finished your mission, allowed your mind to break the hold of the programming."

The doctor was hopeful that Sheppard's questions meant he was beginning to think more clearly and was just a little less mired in his mistaken belief of being culpable.

"How could I remember what to do if I can't remember why I did it?

They shrugged. Beckett ventured, "I haven't read all of the research files. It could be that the conditioning programs the action into the brain that…that…is…"

"Triggered by the signal!" McKay finished, snapping his fingers. "We don't know when Richardson turned it on. We just assumed it'd been going the whole time."

Sheppard looked at McKay, licking his lips. "You said it sounded like Morse code? What did it say?"

"I don't know. I haven't been able to decipher it yet." McKay shrugged. "It repeats every 22 seconds. I've run it through every translator and decryption program we have, but there's nothing. I'm hoping that we find out what it is once all the files have been reviewed."

"Could it just be a random signal that was used to reinforce the programming? Would it actually need to mean something?" Beckett said as he picked up the data pad and turned it on.

McKay nodded thoughtfully. "Possibly. Kind of like Pavlov's dog."

"Rodney!" Elizabeth glared at him.

He realized what he said. "Oh, no! I didn't mean…no…Sorry."

"There were no rewards in this case, Rodney." Beckett said sternly.

"I said I was sorry." He was genuinely contrite as he looked at Sheppard. "I didn't mean you're like…"

"What did it sound like?" Sheppard interrupted him. Now his hands gripped the arms of the chair. For the first time in the conversation, Beckett saw emotion in his patient.

"What?"

"The code. What did it sound like?"

"Oh. Similar to Morse, but it wasn't real. Why?"

Sheppard turned to Beckett. He was worried, even scared. "Could I do it again? Or something else? What if they send someone here with the same signal, or another one?"

"I didn't see anything in the files about it, but I don't think so. From what I've seen so far, they just didn't have time to do more than this one thing." Beckett spoke slowly as he thought about it. "We have to give the people back on Earth time to finish the search and go through all of the files they found. It's going to take me another day or so just to get through what Evan brought back."

"Rodney, you said you have it." Sheppard inclined his head toward the laptop. "Is it on there?"

McKay looked from Sheppard to the laptop and back. "Yes, I have it recorded on here, but I don't know if that's a good idea. Carson?"

"No," Elizabeth and Beckett said together. The doctor continued. "It is not a good idea. Maybe later, in a few days, but not now."

"Carson, I need to know." Sheppard was somewhere between demanding and pleading. The mask was crumbling and they could see he was desparate.

Beckett hated to do this to him, but he shook his head sadly. "Not today. When I know your system is clear of the drugs, we can talk about it. I want you to be stronger and in control when you hear it. Okay?"

Sheppard swallowed hard. As much as he hated to admit it, he knew the doctor was right. His head was just fuzzy enough to make it dangerous to risk it now. He nodded. "Okay."

----------

"We need to play the signal to him, to see if anything happens." McKay followed Elizabeth out of the infirmary.

"Yes, Rodney. I know. I'm sure Carson knows that, too." She stepped into a transporter and winced inwardly when he followed. "He's right, though. We have to give John a chance to get better before we try it."

"I know." He conceded. "I'm just saying it needs to be done."

They exited the transporter and walked towards her office.

She looked at him. "I don't think we could stop John from listening to that signal even if we wanted to."

----------

Sheppard walked slowly, but impatiently, around the main infirmary room. The gunshot wound was healing, but it was still sore and did not yet allow him to move with ease or speed. That in itself was aggravating.

His guards still hovered nearby, and would until Beckett and Elizabeth called them off. Even though he agreed they had to be there and they kept a low profile, the colonel was getting tired of their constant presence. He approached Ronon.

"That thing is set on stun isn't it?"

The Satedan was leaning against a bed. He pulled his weapon from its holster and turned it so that Sheppard could see the setting. After Sheppard turned away, he slid it back into the holster and crossed his arms. His friend was still closed off. Ronon was reminded of how, when he was a runner, he felt every time he entered a village knowing that he was risking everyone there.

Beckett entered with Kate Heightmeyer. She immediately sat quietly to one side, wanting to observe unobtrusively.

"Where is Rodney?" The doctor checked his watch. He walked to the door and spoke to the guards. "Come back in an hour. Ronon will keep an eye on Col. Sheppard until then."

"Yes, Sir." The young men hesitated only briefly. They knew the big Satedan was more than capable of subduing their recovering CO. They disappeared.

"I'm here, I'm here." The astrophysicist said as he hurried in with his laptop. He pulled an over-bed table across the room and set the computer on it. A small speaker appeared from his jacket pocket and he quickly plugged it in.

Sheppard glanced at McKay several times as he paced around the room. There was more than a hint of anxiety in his expression and voice. He was uncertain of himself and how his friends felt about him, about everything.

It was a little more than ten days since Sheppard nearly destroyed the city. According to the good doctor, his body was now free of the drugs and the wound was healing well. His appetite was returning, too. Beckett, along with Kate, finally gave the green light for him to listen to the recorded signal. If all went well, he would be released from the infirmary in a day or two.

"Okay, all set." McKay announced as he turned from the laptop. He looked at Sheppard with a concerned frown. "Ready?"

"Yeah."

Beckett pointed to a chair. "I want you to sit down."

Sheppard glowered at him. "I'm fine."

"No, you're not." The doctor insisted. "This won't happen until you sit down."

"Okay, okay." The colonel exhaled heavily and sat on the chair. He glanced at Ronon, who now cradled his weapon with both hands.

Beckett pulled a chair closer to Sheppard and sat down as well. He nodded at McKay. "Okay."

"Right." McKay nodded nervously and pressed a key on the computer. The faint sound was barely audible. He quickly turned up the volume and said, "Sorry."

Sheppard closed his eyes, head bowed. The others listened in silence to the rhythmic tapping noise, looking from the speaker to the colonel. He didn't move, but they could see a frown deepening on his face.

After a full minute, Sheppard looked up at McKay. His voice was tight. "Turn it off, Rodney."

"What? Oh, yes." He hit a key and the clicking noise stopped.

Sheppard closed his eyes for a moment and rubbed his right temple. He was very pale and breathing fast.

"What is it?" Beckett ducked down to look at his face. "John?"

He shook his head and let his hand fall into his lap. "It's not really Morse. It's a recognition code, well several. They're made up."

"Excuse me?"

Sheppard looked sick. "They're recognition codes. They were just groups of numbers we made up for a couple of missions. If one of them was at the tail end of a transmission, we all knew who the information was from and it was legitimate."

"How did these guys get a hold of them?" McKay was skeptical.

"They're probably in the ops files and the Trust would have access to them."

"Yes, of course." McKay said with disgust. "Just like they have access to our reports."

The headache, which had diminished to a dull throbbing, began to pound again. The black cloud of doubt closed tighter around him. The codes prompted flashes of something in his mind. They were glimpses so brief that it was impossible to separate and make sense of them. It was like watching a battlefield at midnight when only the flash of weapons fire provided light. He stared at the floor, trying to fix them in his mind before they disappeared.

"Col. Sheppard, what is it?"

"John?" Beckett leaned close. Sheppard looked like he'd seen a ghost. "What's wrong?"

"Just remembered something."

"What?" McKay asked.

"I'm not sure. It was just flashes of…of…I think it was when I was on Earth. It was too fast." He licked dry lips.

"Colonel?" Kate spoke for the first time. Apart from the moment they first heard the tapping, she had watched him closely. It was difficult to tell what affected him more, hearing the mechanism used to trigger his actions or recognizing them as something from his past.

He sat upright and looked back at her. "I'm okay. I'm not going to run out and blow the place up, if that's what you're worried about."

Her warm expression didn't change. "No, I wasn't worried about that. I…"

"You should be." Sheppard interrupted her. "We still don't know for sure if I could do it again or if they put anything else in my head."

Beckett sighed. He knew Sheppard was rattled to his core and that it would be difficult to reassure him. "Well, I've been through the files more thoroughly over the last two days. I'm certain Coleman didn't have enough time to give you any other instructions. He wasn't even able to make sure you would complete the task you were supposed to do. John, the whole focus was on the one thing, nothing else. Please believe me. You don't have to worry about it."

"The SGC is analyzing all of the files. Lorne said they're supposed to give us an update during the check-in tomorrow." McKay suggested hopefully. It was painful to see his friend like this.

Sheppard wasn't convinced.

"Colonel, we can work with this." Kate was also hopeful. "We may be able to use these...codes to determine if there is any danger that you will make another attempt. It is possible that they could help you recover some of your memory, too."

He looked at her, a small glimmer of hope finally appearing in his eyes.

"John, you were heavily drugged when this happened. You would never have tried it otherwise." Beckett jumped to reinforce the idea. "Look, it's going to be a few weeks before you are physically able to go on any missions. We have plenty of time to sort this out. You have to give it a chance. Okay?"

"You don't have anything to lose." Ronon said matter-of-factly.

Sheppard nodded thoughtfully. "True."


	6. Chapter 6

"Ah, there you are!" McKay walked quickly to catch up to the colonel. He squinted in the bright sunshine, wishing he'd brought sunglasses like Sheppard was wearing. "You know, you should really tell someone where you're going."

"I did, Rodney, and my two friends always know where I am." Sheppard jerked his thumb towards the Marines that followed about ten yards back. "Ronon's gonna be here in a moment, anyway."

"Oh." McKay said by way of apology. He looked around. The expanse of ocean was almost overwhelming when he came out to one of the piers at water level. It was too wide and far too deep. He needed to look back at the city to feel a modicum of safety.

Sheppard continued walking, and McKay fell in step. The colonel enjoyed the openness out here. The sound of the water moving beneath and around them was soothing. The air was clean and smelled like it. He could remember the smell of Earth and found the memory distasteful.

"Did you want something?"

"No, well, no. I…uh, just wanted to see how you were doing."

"I'm doing fine, thanks." He suppressed a grin as looked sideways at the astrophysicist. The bleak darkness that haunted him for days had finally lifted. As the doctors assured him, he was gaining perspective with the passage of time, and more than a few sessions with Kate Heightmeyer. Feeling physically better and being out of the infirmary also helped.

"So, you're not going back to Earth?" McKay asked hesitantly.

He sighed. "I don't know, Rodney. I should, but it looks like it's up to the brass."

"Well, I don't understand why you keep on insisting that you should go. What happened is not your fault."

Sheppard stopped and turned to him. "Rodney, these guys turned my head inside out and screwed around with it! I know I couldn't help it, but I almost destroyed this city and everyone in it. I should be court-martialed."

"Well, you're wrong about that." McKay kept his voice low, but he was vehement. "You did not do that. It was not you. It was someone the Trust created that did it. That person is gone. You are not that person."

Sheppard took off his sunglasses to look at his friend. He was taken aback and didn't know what to say. "Thanks. I hope you're right."

----------

"Do you have a moment?"

Beckett looked up from his computer to see Elizabeth standing in the doorway.

"Certainly. Please take a seat." He smiled tiredly. It had been another long day. One of the off-world teams had come back with two injuries. Nothing serious, but on top of a particularly contagious flu now going around, the infirmary was busy.

"How is he?" She asked as she sat down.

He was blank for a moment. "Ah, yes. John is doing fine all things considered. He hasn't talked to you?"

"No. He hasn't said much at all."

"Well, I know he's been outside at lot walking, to get some exercise. He's trying to catch up after being in here for so long. And, Kate has him for two or three hours a day."

"Are they getting anywhere?" She asked.

There had been little useful information from Earth in the week since Lorne returned. The two check-ins revealed only that almost all of the Trust members involved escaped and the victims were still being picked up. Nothing new was found that would help the colonel.

One positive piece of information was that no charges would be filed against Sheppard. The IOA and SGC concluded that, provided he was cleared to return to duty by Beckett and Kate Heightmeyer, he could keep his posting in Atlantis. Elizabeth suspected that O'Neill and Landry had a very large say in that.

"Some. John is finally beginning to accept the fact that he had no control of his actions. I don't think he'll ever be completely okay in that respect, but he's coming around. His memory is a different prospect. I doubt he'll ever recover more than a little here and there."

"Why not?"

"The latest report from Earth indicates that the drug cocktail he was given makes it nearly impossible to retain any conscious memories." He paused for a moment, thinking. "The closest analogy I can give you is like someone on a drunken binge. They are so impaired, the memories just weren't laid down."

"Would the za'tarc detector help?" Elizabeth offered.

He shook his head. "No. Rodney's been asking about that. I will not allow that thing to be used on John. It would serve no useful purpose and would probably do a great deal of harm. We know what John did, and that he was conditioned to do it. End of story."

She nodded in agreement, inwardly relieved. She dreaded the thought of using the machine on him. "Do you think he'll try to do it again? I mean, do you think he will be alright?"

Beckett blinked at the question. "No, he won't try it again and, yes, he'll be alright. John is too well-balanced and intelligent not to come to terms with this, and Kate will keep working with him. It'll take some time, but at least we have it."

"Yes, we do." She got up to leave. "It was close."

"Closer than you think." He nodded slowly and stood up, too. "Just between you and me, I'm actually quite amazed that John was able to break through the conditioning and stop the overload. Even given the fact that Coleman felt he needed more time to reinforce it, the conditioning was complete."

The End


End file.
